Fiji Is Just ImageJ
QR for this pageFrom Fiji
![The TrakEM2 plugin provides the means to [http://www.ini.uzh.ch/~acardona/trakem2_manual.html#trees reconstruct neuronal arbors in 3D], including [http://www.ini.uzh.ch/~acardona/trakem2_manual.html#connectors relationships between trees] to represent synapses.](/images/8/86/TrakEM2_neuronal_reconstruction-snapshot.png) |
| The TrakEM2 plugin provides the means to reconstruct neuronal arbors in 3D, including relationships between trees to represent synapses. |
Fiji is an image processing package. It can be described as a distribution of ImageJ (and ImageJ2) together with Java, Java3D and a lot of plugins organized into a coherent menu structure. Fiji compares to ImageJ as Ubuntu compares to Linux.
The main focus of Fiji is to assist research in life sciences.
For users, Fiji is easy to install and has an automatic update function, bundles a lot of plugins and offers comprehensive documentation.
For developers, Fiji is an open source project hosted in a Git version control repository, with access to the source code of all internals, libraries and plugins, and eases the development and scripting of plugins.
Download Fiji now 
List of Update sites
How to cite Fiji? Who is citing Fiji?
Collaboration
The Fiji project is driven by a strong desire to improve the tools available for life sciences to process and analyze data. To this end, Fiji collaborates closely with the following projects:
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| ImageJ2 | Bio-Formats | OME | µManager | KNIME |
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News
- 2014-03-19 - TrackMate v2.2.0 released
- 2014-03-03 - Fiji shines in ISBI 2012 particle tracking challenge
- 2014-03-03 - Fiji plays Squassh
- 2014-02-04 - Wiki engine upgrade
- 2014-01-25 - MosaicSuite for Fiji
Subscribe to an RSS or Atom feed of the Fiji news.
Browse the news archive.
Documentation
Using Fiji
- What you need to know about scientific image processing
- Installing Fiji
- Getting started with Fiji
- Tutorials (also external ones)
- Find contact information (also how to get an account on this Wiki), mailing list, IRC (chat) and help
- Frequently Asked Questions
- more...
Advanced Fiji usage
- Registering 3D images
- Segmenting images
- Useful keyboard shortcuts
- Scripting: with Macros, in Beanshell, in Javascript, in JRuby, in Jython, in Clojure (see also Scripting Help).
- Some ImageJ tricks
- Links
- more...
Developing for Fiji
- Introduction into Developing Plugins
- Developing ImageJ 1.x plugins with NetBeans
- Developing Fiji (i.e., the Fiji source code itself)
- Developing Fiji in Eclipse (i.e., the Fiji source code itself)
- more...
Projects
- Hardware-accelerated 3D volume and mesh visualization, and 3D registration of image stacks.
- Interactive image transformation (rigid, similarity, affine, perspective, deform)
- Interactive Stack Rotation
- Landmark based transformation and deformation
- Panorama Viewer
- Distortion correction: correct lens deformation induced by the microscope (optical and electron microscopy). See the Distortion Correction plugin manual.
- Elastic Alignment and Montage
- SPIM Registration Registration and fusion of Selective Plane Illumination Microscopy data.
- Image Stitching Stitch multiple image stacks across X,Y,Z,T and C.
- Feature Extraction SIFT and MOPS.
- Consistent and elastic 2D registration (bUnwarpJ)
- Stack slice registration
- Image montage (via TrakEM2) with global optimization (in 2D and across sections)
- VIB Protocol Label-based 3D alignment of image stacks.
- Simple Neurite Tracer (project page)
- Segmentation Editor
- Manual (via TrakEM2)
- Level Sets
- Trainable Segmentation
- SIOX: Simple Interactive Object Extraction
- Analysis
- Generic and extensible n-dimensional image processing library for Java.
- Register/edit/analyze/segment/annotate/3D model terabytes of confocal and electron microscopy images.
- The core of Fiji.
Downloads
Critical: if your updater does not work any longer, please drag & drop this link to your Fiji main window and follow the instructions in the text window. If that does not work, pleasefollow these instructions.
Download
We have continuous releases thanks to ImageJ's Jenkins server:
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| Continuous release | 32-bit | Windows (32-bit) | OS X1 | Linux (32-bit) | N/A | All platforms (no JREs) |
| 64-bit | Windows (64-bit) | Linux (64-bit) | ||||
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[1] There is only limited support for PowerPC (G4/G5) Macs, see MacOSX tips for a special download link. | ||||||
| As announced in this mail, we join the legions of construction workers digging up the streets during the second half of July 2013 (i.e. we also use the slow summer month to break things in order to make them better), incorporating extensive changes to reconcile Fiji with ImageJ2. The packages below reflect Fiji as of July 15th, 2013 and are offered here just in case the continuous build (or an updated version) above broke a formerly working operation that is desperately needed, like, right now. | ||||||
| Life-Line version | 32-bit | Windows (32-bit) | OS X1 | Linux (32-bit) | N/A | All platforms (no JREs) |
| 64-bit | Windows (64-bit) | Linux (64-bit) | ||||
See the Downloads page for debian packages and others.
License
Fiji is released under the General Public License.
Each component has its own license.
